Question: Convert biom to tabular file and parse taxonomic levels
0
gravatar for naphtali.paul
2.4 years ago by
naphtali.paul0 wrote:

Hi all,

I currently have an otu table that was generated from QIIME in the biom format. It comprises of 16S rRNA sequences that were annotated into OTUs. I used the biom convert command to create a tsv file, but the taxonomy names follow the Greengenes guidelines, where taxonomic levels are identified by k__(name); p__(name), and so forth to s__; , the species level.

Is there a flag within the biom commands which lets me parse the taxonomic levels as separate columns in the tsv file? I'm doing this so I can input the tsv table into R to analyze the data with vegan.

Thanks!

qiime biom sequencing • 1.7k views
ADD COMMENTlink modified 2.4 years ago by fanli.gcb650 • written 2.4 years ago by naphtali.paul0
1
gravatar for biokoala
2.4 years ago by
biokoala3.6k
biokoala3.6k wrote:

Did you try this?

> biom convert -i table.biom -o table.from_biom_w_taxonomy.txt --to-tsv --header-key taxonomy

Also, please let me know the exact command you are running.

ADD COMMENTlink written 2.4 years ago by biokoala3.6k
0
gravatar for fanli.gcb
2.4 years ago by
fanli.gcb650
Los Angeles, CA
fanli.gcb650 wrote:

If you are doing 16S analysis with R, you may want to check out the phyloseq package. It has built-in functions for parsing QIIME biom files as well as many other things you'll likely want to do. See https://joey711.github.io/phyloseq/import-data.html#import_biom

ADD COMMENTlink written 2.4 years ago by fanli.gcb650
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